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The point is that contracts can be negotiated before being signed. There's no single, all-encompassing contract that everyone signs.
No studio is investing hundreds of millions of dollars on this project.
It's not a summer blockbuster, it's a small-scale film.
Many misconceptions here.
Some things are not negotiable, about half the revenue from superheroes and similar properties comes form licensing.
It doesn't matter if the studio invested 50 or 400 million on this specific project, the principle is the same, they will not allow anything to get in the way of profit making.
You have no way of knowing how successful this film will be, not that it would change anything to the principles at work.
The notion that the studio needs Phoenix more than he needs them is ridiculous.
No actor is irreplaceable, not one.
The studios know that, so do the actors and the few who fail to get this may see their careers cut short.
There's also the idea that Phoenix or Day-Lewis are the type of guys who wouldn't want to see their likeness on toys because they're "real" actors or "artists".
That is a naive notion, if they agree to work on superhero projects they know what the deal is is.
These guys are professionals first and foremost, they've been in this business for years and know that playing the game is what gets them millions and allows them to do what they like such as acting (or cobbling or whatever it is that Day-Lewis does now).